Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The Ciona notochord transcriptome reveals a core set of broadly conserved notochord effector genes

ABSTRACT: The notochord is the eponymous feature of the chordates and an essential organ in chordate development. The notochord of the invertebrate chordate Ciona consists of only 40 cells, and is a longstanding model for studying differentiation and morphogenesis in a small, simple embryo. Here we perform RNAseq analysis on flow-sorted notochord cells from multiple stages of development to define a comprehensive Ciona notochord transcriptome. We identify 1364 genes with enriched expression in the notochord and extensively validate the results by in situ hybridization. This notochord gene set is highly enriched for Gene Ontology codes related to the extracellular matrix, cell adhesion and cytoskeleton, and contains numerous genes with intriguing potential functions in morphogenesis. Orthologs of 112 of the Ciona notochord genes have known notochord expression in vertebrates, more than twice as many as would be predicted by chance alone. This set of putative effector genes with notochord expression conserved from tunicates to vertebrates will be invaluable for testing hypotheses about the evolution of the notochord.

ORGANISM(S): Ciona intestinalis

PROVIDER: GSE95333 | GEO | 2017/09/19

SECONDARY ACCESSION(S): PRJNA376667

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Brachyury controls Ciona notochord fate as part of a feedforward network [I]

Project description:The notochord is a defining feature of the chordates. The transcription factor Brachyury (Bra) is a key regulator of notochord fate but here we show that it is not a unitary master regulator in the model chordate Ciona. Ectopic Bra expression only partially reprograms other cell types to a notochord-like transcriptional profile and a subset of notochord-enriched genes are unaffected by CRISPR Bra disruption. We identify Foxa.a and Mnx as potential co-regulators and find that combinatorial cocktails are more effective at reprograming other cell types than Bra alone. We reassess the network relationships between Foxa.a, and other components of the notochord gene regulatory network and find that Foxa.a expression in the notochord is regulated by vegetal FGF signaling. It is a direct activator of Bra expression and has a binding motif that is significantly enriched in the regulatory regions of notochord-enriched genes. These and other results indicate that Bra and Foxa.a act together in a regulatory network dominated by positive feed-forward interactions, with neither being a classically-defined master regulator.

2020-10-31 | GSE160544 | GEO

Brachyury controls Ciona notochord fate as part of a feedforward network [IV]

2020-10-31 | GSE160547 | GEO

Brachyury controls Ciona notochord fate as part of a feedforward network [III]

2020-10-31 | GSE160546 | GEO

Brachyury controls Ciona notochord fate as part of a feedforward network [II]

2020-10-31 | GSE160545 | GEO

Ciona savignyi notochord LC-MS/MS based on 4D Mass Spectromete

Project description:Lumen formation and inflation are crucial for tubular organ morphogenesis, yet the underling mechanism remains largely unrevealed. Here, we applied 4D proteomics to screen the lumenogenesis-related proteins and reveal the potentially biological pathways that are involved in lumen inflation during notochord lumen formation in ascidian Ciona savignyi.

2023-05-10 | PXD037089 | Pride

Expression profiling of Ciona intestinalis neurula and mid-tailbud stage embryos expressing altered forms of the transcription factor Ci-Tbx2/3 in the notochord

Project description:Despite being found in the notochord of several chordates, the roles of the Tbx2 subfamily of T-box transcription factors in the development of this tissue remain largely unknown. We explored the targets of the only Tbx2 subfamily member in Ciona intestinalis, Ci-Tbx2/3, by expressing mutant forms of the transcriptional regulator using the Ci-Bra promoter region. We produced a dominant interfering version of Ci-Tbx2/3 (Tbx2/3DBD) through expression of a truncated version consisting only of its DNA-binding domain (DBD) and a constitutive activator form by attaching the T-box of Ci-Tbx2/3 to the VP16 transactivation domain (Tbx2/3VP16). These constructs were introduced into 1-cell stage embryos and grown to the neurula (N) or mid-tailbud (mTb) stage to capture targets regulated throughout notochord morphogenesis. Ci-Tbx2/3 targets were ascertained using whole-genome custom Affymetrix microarrays to compare the transcription levels of Tbx2/3DBD and Tbx2/3VP16 expressing embryos to wild-type controls (Bra>GFP) at the neurula or mTb stages.

2013-04-27 | E-GEOD-42267 | biostudies-arrayexpress

Expression profiling of Ciona intestinalis neurula and mid-tailbud stage embryos expressing altered forms of the transcription factor Ci-Tbx2/3 in the notochord

2013-04-27 | GSE42267 | GEO

Expression profiling of Ciona intestinalis initial tailbud stage embryos expressing mutant forms of the transcription factor Ci-XBP1 in the notochord.

Project description:XBP transcription factors are well-known regulators of the the unfolded protein response and are required for plasma cell differentiation. However, recent studies have shown that the XBP1 gene is also expressed in the developing notochord of Ciona and various vertebrates, and to date its role in the formation of this organ is largely uncharacterized. We identified putative targets of Ci-XBP1 through a microarray screen, using RNAs extracted from embryos expressing mutant forms of this transcriptional regulator in the notochord. We expressed in the Ciona notochord a dominant-negative version of Ci-XBP1 (XBP DBD::GFP) by cloning its DNA-binding domain (DBD) downstream of the Ci-Brachyury (Ci-Bra) promoter. We created a constitutive activator form of Ci-XBP by fusing its DBD to the VP16 transactivation domain (Bra>XBP DBD::VP16::GFP). These constructs were introduced into 1-cell stage embryos and grown to the initial tailbud (iTb) stage to identify Ci-XBP notochord target genes.

2022-01-20 | GSE46751 | GEO

Ectopic expression of the Brachyury transcription factor upregulates only a subset of notochord expressed genes

Project description:The key notochord transcription factor Brachyury was ectopically expressed in Ciona embryos under the control of the FoxAa cis-regulatory region (which drives expression in neural, endodermal and mesenchymal lineages in addition to notochord). Misexpression of Brachyury induced 925 genes compared to a control reporter plasmid (Bra>GFP). There was only modest overlap with a set of notochord-enriched genes previously identified by RNAseq of flow-sorted notochord cells, indicating that Brachyury is not a notochord master regulator gene as strictly defined.

2017-09-19 | GSE102142 | GEO

Transcriptome analysis of Ciona intestinalis to identify genes expressed in the adult organs.

Project description:Among urochordates (tunicates)—the closest living relatives of vertebrates—Ciona intestinalis is increasingly being used as a model organism in the field of developmental biology. Ciona intestinalis is the seventh animal which genome published; the ~120-Mbp euchromatin region is estimated to contain ~16,000 protein-coding genes. In addition, analyses of more than one million ESTs have provided the foundation for gene models and associated transcriptomes. The fertilized Ciona intestinalis egg develops into a tadpole larva with a simplified chordate body plan, and then it metamorphose into adult sea squirt of sessile filter feeder. One of interests in the field of developmental biology is to understand what kind of genes are expressed in the body and how spatially and/or temporally coordinated expression of genes is controlled. In this study, we investigated the entire gene expression of 11 organs of adult Ciona; the neural complex, branchial sac, esophagus, stomach, endostyle, intestine, body-wall muscle, heart, blood cells, ovary, and testis. Our data would provides basic information of transcriptome in each organ and help to understand gene expression control of organ specific genes.

2010-10-27 | GSE24941 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data